plotSegment: Plot segmentation.

In SomatiCA: SomatiCA: identifying, characterizing, and quantifying somatic copy number aberrations from cancer genome sequencing

Description

Plot segmentation.

Usage

plotSegment(segment, input, k = 1, col1 = "orange", col2 = "blue", smooth = FALSE, dev.new = TRUE, cex.point =0.5, ...)

Arguments

segment	A GRanges object, segmentation result.
input	A GRanges object, input for SomatiCA.
k	When there are multiple chromosomes, only kth will be plot each time.
col1	Color for data points.
col2	Color for segments.
smooth	Whether smoothed data is plotted. Default is T.
dev.new	Whether a new device will be opened.
cex.point	Size of data points.
...	Parameters in plot().

Value

A plot.

Author(s)

Mengjie Chen

Examples

#data#
rawLAF <- c(rnorm(300, 0.2, 0.05), rnorm(300, 0.4, 0.05), rnorm(200, 0.3, 0.05), rnorm(200, 0.2, 0.05), rnorm(200, 0.3, 0.05), rnorm(250, 0.4, 0.05)) 
reads <- rep(50, 800+650)
chr <- c(rep("chr1", 800), rep("chr2", 650))
position <- c(c(1:800), c(1:650))
zygo <- rep("het", 800+650)
input <- GRanges(seqnames=chr, 
                 ranges=IRanges(start=position, width=1), 
                 zygosity=zygo, 
                 tCount=reads, 
                 LAF=rawLAF, 
                 tCountN=reads, 
                 gLAF=rawLAF) 
                 
#segment#
chr <- c("chr1", "chr1", "chr1", "chr2", "chr2", "chr2")
start <- c(1, 300, 600, 1, 200, 400) 
end <- c(300, 600, 800, 200, 400, 650)
medLAF <- c(0.2, 0.4, 0.3, 0.2, 0.3, 0.4)
medgermlineLAF <- rep(0.4, 6)
segment <- GRanges(seqnames=chr, 
                   ranges=IRanges(start=start, end=end), 
                   medLAF=medLAF, 
                   medgLAF=medgermlineLAF)

## First chromosome
plotSegment(segment, input, k=1)
## Second chromosome
plotSegment(segment, input, k=2)

SomatiCA documentation built on Oct. 5, 2016, 4:18 a.m.